From the command line it gives the following warnings about things
that it can’t find. (Sorry for the massive text dump… a lot of this
doesn’t really mean that much to me so it’s hard to tell what’s
important)
Chris
warning: Unable to read symbols for “QtOpenGL.framework/Versions/4/
QtOpenGL” (file not found).
warning: Unable to read symbols from “QtOpenGL” (not yet mapped into
memory).
warning: Unable to read symbols for “QtGui.framework/Versions/4/
QtGui” (file not found).
warning: Unable to read symbols from “QtGui” (not yet mapped into
memory).
warning: Unable to read symbols for “QtNetwork.framework/Versions/4/
QtNetwork” (file not found).
warning: Unable to read symbols from “QtNetwork” (not yet mapped into
memory).
warning: Unable to read symbols for “QtCore.framework/Versions/4/
QtCore” (file not found).
warning: Unable to read symbols from “QtCore” (not yet mapped into
memory).
Reading symbols for shared libraries .
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/atom.o” - no debug information available for “atom.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/alias.o” - no debug information available for “alias.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/base.o” - no debug information available for “base.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/bitvec.o” - no debug information available for “bitvec.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/bond.o” - no debug information available for “bond.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/bondtyper.o” - no debug information available for
“bondtyper.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/canon.o” - no debug information available for “canon.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/builder.o” - no debug information available for “builder.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/chains.o” - no debug information available for “chains.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/chiral.o” - no debug information available for “chiral.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/data.o” - no debug information available for “data.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/descriptor.o” - no debug information available for
“descriptor.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/fingerprint.o” - no debug information available for
“fingerprint.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/forcefield.o” - no debug information available for
“forcefield.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/format.o” - no debug information available for “format.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/generic.o” - no debug information available for “generic.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/griddata.o” - no debug information available for
“griddata.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/grid.o” - no debug information available for “grid.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/locale.o” - no debug information available for “locale.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/kekulize.o” - no debug information available for
“kekulize.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/matrix.o” - no debug information available for “matrix.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/mol.o” - no debug information available for “mol.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/molchrg.o” - no debug information available for “molchrg.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/obconversion.o” - no debug information available for
“obconversion.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/oberror.o” - no debug information available for “oberror.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/obiter.o” - no debug information available for “obiter.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/obmolecformat.o” - no debug information available for
“obmolecformat.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/obutil.o” - no debug information available for “obutil.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/op.o” - no debug information available for “op.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/ops.o” - no debug information available for “ops.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/parsmart.o” - no debug information available for
“parsmart.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/patty.o” - no debug information available for “patty.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/phmodel.o” - no debug information available for “phmodel.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/plugin.o” - no debug information available for “plugin.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/pointgroup.o” - no debug information available for
“pointgroup.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/rand.o” - no debug information available for “rand.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/residue.o” - no debug information available for “residue.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/ring.o” - no debug information available for “ring.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/rotor.o” - no debug information available for “rotor.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/rotamer.o” - no debug information available for “rotamer.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/tokenst.o” - no debug information available for “tokenst.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/typer.o” - no debug information available for “typer.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/transform.o” - no debug information available for
“transform.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/dlhandler_unix.o” - no debug information available for
“dlhandler_unix.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libmath.a/matrix3x3.o” - no debug
information available for “matrix3x3.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libmath.a/spacegroup.o” - no debug
information available for “spacegroup.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libmath.a/transform3d.o” - no debug
information available for “transform3d.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libmath.a/vector3.o” - no debug information
available for “vector3.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libfingerprints.a/finger2.o” - no debug
information available for “finger2.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libfingerprints.a/finger3.o” - no debug
information available for “finger3.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libforcefields.a/forcefieldghemical.o” - no
debug information available for “forcefieldghemical.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libforcefields.a/forcefieldmmff94.o” - no
debug information available for “forcefieldmmff94.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libforcefields.a/forcefielduff.o” - no
debug information available for “forcefielduff.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libops.a/addpolarh.o” - no debug
information available for “addpolarh.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libops.a/fillUC.o” - no debug information
available for “fillUC.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libops.a/gen3d.o” - no debug information
available for “gen3d.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libops.a/loader.o” - no debug information
available for “loader.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libops.a/optransform.o” - no debug
information available for “optransform.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libdescriptors.a/cmpdfilter.o” - no debug
information available for “cmpdfilter.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libdescriptors.a/filters.o” - no debug
information available for “filters.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libdescriptors.a/groupcontrib.o” - no debug
information available for “groupcontrib.cpp”.
warning: Could not find object file “/Volumes/Home/ghutchis/Devel/ob22/
src/.libs/libopenbabel.lax/libdescriptors.a/smartsdescriptors.o” - no
debug information available for “smartsdescriptors.cpp”.
On Nov 1, 2009, at 5:43 PM, Marcus D. Hanwell wrote:
Williams wrote:
It’s definitely something weird with regard to the directory layout.
If you try to run it out of the build directory it starts but gives a
gives a dialogue box with the message
No tools or engines loaded. It is unlikely this application will
function correctly. Please correct this error.
If you could run it from a shell compiled with debug output then it
should spit out the directories it is searching for plugins in. My
guess
is that I broke the relative layout, and if you can copy and paste
those
lines I should be able to get it fixed up.
Looking in the Avogadro.app/Contents/ directory I find it has only
the
directories:
Info.plist MacOS
That is fine - there is logic in Avogadro to figure out it is in a
build
directory, and use a different directory layout. All of the libs are
in
the lib subdirectory of the build directory.
as opposed to the working installed version which has:
Info.plist MacOS Resources include lib share
I tried moving the appropriate directories into the local version
manually but then it just quit unexpectedly on startup. Also if you
use the cmake command
Not sure why it quit, but moving things around like that is unlikely
to
work.
-DCMAKE_INSTALL_PREFIX=/Users/Williams/Software/AvagadroClean/Test
then grepping in all files for ‘/Users/Williams/Software/
AvagadroClean/
Test’ gives
AvogadroBuildSettings.cmake:SET(CMAKE_BUILD_SETTING_BUILD_TYPE “/
Users/
Williams/Software/AvagadroClean/Test”)
CMakeCache.txt:CMAKE_BUILD_TYPE:STRING=/Users/Williams/Software/
AvagadroClean/Test
CMakeCache.txt:QT_QTTEST_INCLUDE_DIR:PATH=/Library/Frameworks/
QtTest.framework/Headers
CMakeCache.txt:QT_QTTEST_LIBRARY:STRING=optimized;/Library/
Frameworks/
QtTest.framework;debug;/Library/Frameworks/QtTest.framework
CMakeCache.txt:QT_QTTEST_LIBRARY_RELEASE:FILEPATH=/Library/
Frameworks/
QtTest.framework
CMakeCache.txt://Test COMPILES_WITHOUT_FPERMISSIVE
CMakeCache.txt://Test HAVE_GCC_VISIBILITY
cmake_install.cmake: SET(CMAKE_INSTALL_CONFIG_NAME “/Users/
Williams/
Software/AvagadroClean/Test”)
but grepping for ‘/Applications/Avogadro.app/Contents’ gives
AvoCPackOptions.cmake:# New apple packaging stuff
AvogadroConfig.cmake:set(Avogadro_INSTALL_PREFIX “/Applications/
Avogadro.app/Contents”)
AvogadroConfig.cmake:set(Avogadro_INCLUDE_DIRS “/Applications/
Avogadro.app/Contents/include”)
AvogadroConfig.cmake:set(Avogadro_LIBRARY_DIRS “/Applications/
Avogadro.app/Contents/lib”)
AvogadroConfig.cmake:set(Avogadro_PLUGIN_DIR “/Applications/
Avogadro.app/Contents/lib/avogadro/1_1”)
AvogadroConfig.cmake:set(Avogadro_BIN_DIRS “/Applications/
Avogadro.app/Contents/bin”)
cmake_install.cmake: SET(CMAKE_INSTALL_PREFIX “/Applications/
Avogadro.app/Contents”)
Overall it looks like there’s some problems with the cmake scripts
not
setting everything to the right value. What do you think is the best
way to proceed? If I manage to get the right directories in bin/
Avogadro.app/Contents/ in the build directory will everything be OK?
Part of the problem is with caching - if you just try to change these
things and rerun cmake a lot of the variables are cached and will
not be
changed. This is a bug I need to spend some time fixing. You need to
delete the CMakeCache.txt file in the build directory, or start with a
fresh build directory. That Mac has a different directory layout to
the
other platforms, but I am 99% certain the installed Avogadro should
work
without issue (this receives the most testing).
I think only a few people like me ran Avogadro from the command
line. So
that may not work correctly. You would have to let me see the output
from Avogadro on the command line to see where it is searching for
things. I kept promising to make an extension that dumped this stuff
to
a useful debug text file, but never found the time to do it.
You may have more success starting with a clean build directory with
the
install prefix you would like to use. I worked quite hard to get
Avogadro on the Mac to just use a single app directory, before that it
was installing half its files into /usr/local… The released app runs
install_name_tool to give relative references to libraries, but this
step is quite slow. This allows the final app to be relocated, but
that
final step is still quite clunky.
I hope this makes things a little clearer. There are still some issues
that need cleaning up, and I would like to fix the running from the
build dir on Mac if I can.
Marcus